/*
* This file is part of JGAP.
*
* JGAP offers a dual license model containing the LGPL as well as the MPL.
*
* For licensing information please see the file license.txt included with JGAP
* or have a look at the top of class org.jgap.Chromosome which representatively
* includes the JGAP license policy applicable for any file delivered with JGAP.
*/
package org.jgap;
import org.jgap.util.StringKit;
/**
* Abstract base class for all genes. Provides default implementations.
*
* @author Klaus Meffert
* @since 2.2
*/
public abstract class BaseGene
implements Gene, IBusinessKey {
/** String containing the CVS revision. Read out via reflection!*/
private final static String CVS_REVISION = "$Revision: 1.27 $";
/**
* Delta, useful for comparing doubles and floats.
*/
public static final double DELTA = 0.0000001;
/** Energy of a gene, see RFE 1102206*/
private double m_energy;
/**
* Application-specific data that is attached to the Gene. This data may
* assist the application in labelling this Gene.
* JGAP ignores the data, aside from allowing it to be set and
* retrieved and considering it in clone() and compareTo().
*
* @since 2.4
*/
private Object m_applicationData;
/**
* Method compareTo(): Should we also consider the application data when
* comparing? Default is "false" as "true" means a Gene's losing its
* identity when application data is set differently!
*
* @since 2.4
*/
private boolean m_compareAppData;
private Configuration m_configuration;
/**
* Constants for toString()
*/
public final static String S_APPLICATION_DATA = "Application data";
/**
*
* @param a_configuration the configuration to use
* @throws InvalidConfigurationException
*
* @author Klaus Meffert
* @since 3.0
*/
public BaseGene(Configuration a_configuration)
throws InvalidConfigurationException {
if (a_configuration == null) {
throw new InvalidConfigurationException("Configuration must not be null!");
}
m_configuration = a_configuration;
}
/**
* Retrieves the allele value represented by this Gene.
*
* @return the allele value of this Gene
* @since 1.0
*/
public Object getAllele() {
return getInternalValue();
}
/**
* Retrieves the hash code value for a Gene.
* Override if another hashCode() implementation is necessary or more
* appropriate than this default implementation.
*
* @return this Gene's hash code
*
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public int hashCode() {
// If our internal value is null, then return zero. Otherwise,
// just return the hash code of the allele Object.
// -----------------------------------------------------------
if (getInternalValue() == null) {
return -79;
}
else {
return getInternalValue().hashCode();
}
}
/**
* Executed by the genetic engine when this Gene instance is no
* longer needed and should perform any necessary resource cleanup.
* If you need a special cleanup, override this method.
*
* @author Klaus Meffert
* @since 1.0
*/
public void cleanup() {
// No specific cleanup is necessary by default.
// --------------------------------------------
}
/**
* Retrieves a string representation of this Gene's value that
* may be useful for display purposes.
*
* @return a string representation of this Gene's value
*
* @author Klaus Meffert
* @since 1.0
*/
public String toString() {
String representation;
if (getInternalValue() == null) {
representation = "null";
}
else {
representation = getInternalValue().toString();
}
String appData;
if (getApplicationData() != null) {
appData = getApplicationData().toString();
}
else {
appData = "null";
}
representation += ", " + S_APPLICATION_DATA + ":" + appData;
return representation;
}
/**
* @return the size of the gene, i.e the number of atomic elements. Always 1
* for non-composed Gene types. Override for composed Gene types
*
* @author Neil Rotstan
* @since 1.0
*/
public int size() {
return 1;
}
/**
* Compares this Gene with the given object and returns true if the other
* object is a Gene of the same type and has the same value (allele) as
* this Gene. Otherwise it returns false.
*
* @param a_other the object to compare to this Gene for equality
* @return true if this Gene is equal to the given object, false otherwise
*
* @author Klaus Meffert
* @since 1.1
*/
public boolean equals(final Object a_other) {
try {
int result = compareTo(a_other);
if (result == 0) {
if (isCompareApplicationData()) {
Gene otherGene = (Gene) a_other;
int resultAppData = compareApplicationData(getApplicationData(),
otherGene.getApplicationData());
return resultAppData == 0;
}
else {
return true;
}
}
else {
return false;
}
} catch (ClassCastException e) {
// If the other object isn't an Gene of current type
// (like IntegerGene for IntegerGene's), then we're not equal.
// -----------------------------------------------------------
return false;
}
}
/**
* Each Gene implementation holds its own m_value object keeping the allele
* value. In your Gene implementation, just return it with this method
* (see {@link org.jgap.impl.BooleanGene} for example)
* @return the m_value object
*
* @author Klaus Meffert
* @since 2.2
*/
protected abstract Object getInternalValue();
/**
* @return energy of the gene
*
* @author Klaus Meffert
* @since 2.3
*/
public double getEnergy() {
return m_energy;
}
/**
* Sets the energy of the gene
* @param a_energy the energy to set
*
* @author Klaus Meffert
* @since 2.3
*/
public void setEnergy(final double a_energy) {
m_energy = a_energy;
}
/**
* This sets the application-specific data that is attached to this Gene.
* Attaching application-specific data may be useful for
* some applications when it comes time to distinguish a Gene from another.
* JGAP ignores this data functionally.
*
* @param a_newData the new application-specific data to attach to this
* Gene
*
* @author Klaus Meffert
* @since 2.4
*/
public void setApplicationData(final Object a_newData) {
m_applicationData = a_newData;
}
/**
* Retrieves the application-specific data that is attached to this Gene.
* Attaching application-specific data may be useful for
* some applications when it comes time to distinguish a Gene from another.
* JGAP ignores this data functionally.
*
* @return the application-specific data previously attached to this Gene,
* or null if there is no data attached
*
* @author Klaus Meffert
* @since 2.4
*/
public Object getApplicationData() {
return m_applicationData;
}
/**
* Should we also consider the application data when comparing? Default is
* "false" as "true" means a Gene is losing its identity when
* application data is set differently!
*
* @param a_doCompare true: consider application data in method compareTo
*
* @author Klaus Meffert
* @since 2.4
*/
public void setCompareApplicationData(final boolean a_doCompare) {
m_compareAppData = a_doCompare;
}
/*
* @return should we also consider the application data when comparing?
*
* @author Klaus Meffert
* @since 2.4
*/
public boolean isCompareApplicationData() {
return m_compareAppData;
}
protected int compareApplicationData(final Object a_appdata1,
final Object a_appdata2) {
// Compare application data.
// -------------------------
if (a_appdata1 == null) {
if (a_appdata2 != null) {
return -1;
}
else {
return 0;
}
}
else if (a_appdata2 == null) {
return 1;
}
else {
// The above code is contained in the following, but for performance
// issues we keep it here redundantly.
// -----------------------------------------------------------------
ICompareToHandler handler = getConfiguration().getJGAPFactory().
getCompareToHandlerFor(a_appdata1, a_appdata2.getClass());
if (handler != null) {
try {
return ( (Integer) handler.perform(a_appdata1, null, a_appdata2)).
intValue();
} catch (Exception ex) {
throw new Error(ex);
}
}
else {
return 0;
}
}
}
/**
* Optional helper class for checking if a given allele value to be set
* for a given gene is valid. If not, the allele value may not be set for the
* gene or the gene type (e.g. IntegerGene) is not allowed in general!
*
* @since 2.5 (moved from CompositeGene, where it was since 2.0)
*/
private IGeneConstraintChecker m_geneAlleleChecker;
/**
* Sets the constraint checker to be used for this gene whenever method
* setAllele(Object) is called.
* @param a_constraintChecker the constraint checker to be set
*
* @author Klaus Meffert
* @since 2.5 (moved from CompositeGene, where it was since 2.0)
*/
public void setConstraintChecker(
final IGeneConstraintChecker a_constraintChecker) {
m_geneAlleleChecker = a_constraintChecker;
}
/**
* @return IGeneConstraintChecker the constraint checker to be used whenever
* method setAllele(Object) is called.
*
* @author Klaus Meffert
* @since 2.5 (moved from CompositeGene, where it was since 2.0)
*/
public IGeneConstraintChecker getConstraintChecker() {
return m_geneAlleleChecker;
}
/**
* Provides implementation-independent means for creating new Gene
* instances. The new instance that is created and returned should be
* setup with any implementation-dependent configuration that this Gene
* instance is setup with (aside from the actual value, of course). For
* example, if this Gene were setup with bounds on its value, then the
* Gene instance returned from this method should also be setup with
* those same bounds. This is important, as the JGAP core will invoke this
* method on each Gene in the sample Chromosome in order to create each
* new Gene in the same respective gene position for a new Chromosome.
*
* @return a new Gene instance of the same type and with the same setup as
* this concrete Gene
*
* @author Neil Rostan
* @author Klaus Meffert
* @since 2.6 (since 1.0 in IntegerGene)
*/
public Gene newGene() {
Gene result = newGeneInternal();
result.setConstraintChecker(getConstraintChecker());
result.setEnergy(getEnergy());
/**@todo clone app.data*/
result.setApplicationData(getApplicationData());
return result;
}
protected abstract Gene newGeneInternal();
/**
* @return the configuration set
*
* @author Klaus Meffert
* @since 3.0
*/
public Configuration getConfiguration() {
return m_configuration;
}
public String getBusinessKey() {
Object allele = getAllele();
String result = getClass().getName() + PERSISTENT_FIELD_DELIMITER;
if (allele == null) {
return result;
}
return result + allele.toString();
}
protected String encode(String a_string) {
return StringKit.encode(a_string);
}
protected String decode(String a_string) {
return StringKit.decode(a_string);
}
}
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